Changes

 Summary of important user-visible changes for BioPerl
 -----------------------------------------------------
 
+1.7.5     2019-02-11 14:57:45+00:00 Europe/London
+
+    * The following modules have been removed from the BioPerl
+      distribution to be part of a separate distribution with
+      independent development:
+
+          Bio::Symbol::*
+
+    * The Bio::Seq::SeqWithQuality module, which was deprecated since
+      2001, was finally removed.
+
+    * The deprecated() method has been deprecated.  It is recommended
+      to use Carp::carp to warn.
+
+    * The following methods have been deprecated for a long while and
+      have now been removed:
+
+          Bio::Align::AlignI->no_residues
+          Bio::Align::AlignI->no_sequences
+          Bio::LocatableSeq->no_gap
+          Bio::LocatableSeq->no_sequences
+          Bio::SeqFeature::Generic->slurp_gff_file
+          Bio::SimpleAlign->no_residues
+          Bio::SimpleAlign->no_sequences
+
+
 1.7.4     2019-02-05 16:23:53+00:00 Europe/London
 
     * Fix Bio::Root::Test, and the testuite, to properly check for

MANIFEST

@@ -386,7 +386,6 @@ lib/Bio/Seq/RichSeqI.pm
 lib/Bio/Seq/SeqBuilder.pm
 lib/Bio/Seq/SeqFactory.pm
 lib/Bio/Seq/SeqFastaSpeedFactory.pm
-lib/Bio/Seq/SeqWithQuality.pm
 lib/Bio/Seq/SequenceTrace.pm
 lib/Bio/Seq/SimulatedRead.pm
 lib/Bio/Seq/TraceI.pm
@@ -469,13 +468,6 @@ lib/Bio/SeqUtils.pm
 lib/Bio/SimpleAlign.pm
 lib/Bio/SimpleAnalysisI.pm
 lib/Bio/Species.pm
-lib/Bio/Symbol/Alphabet.pm
-lib/Bio/Symbol/AlphabetI.pm
-lib/Bio/Symbol/DNAAlphabet.pm
-lib/Bio/Symbol/ProteinAlphabet.pm
-lib/Bio/Symbol/README.Symbol
-lib/Bio/Symbol/Symbol.pm
-lib/Bio/Symbol/SymbolI.pm
 lib/Bio/Taxon.pm
 lib/Bio/Tools/Alignment/Consed.pm
 lib/Bio/Tools/Alignment/Trim.pm
@@ -531,7 +523,6 @@ lib/Bio/Tools/Run/AnalysisFactory.pm
 lib/Bio/Tools/Run/GenericParameters.pm
 lib/Bio/Tools/Run/ParametersI.pm
 lib/Bio/Tools/Run/Phylo/PhyloBase.pm
-lib/Bio/Tools/Run/README
 lib/Bio/Tools/Run/WrapperBase.pm
 lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
 lib/Bio/Tools/Seg.pm
@@ -578,32 +569,6 @@ lib/Bio/TreeIO/tabtree.pm
 lib/Bio/UpdateableSeqI.pm
 lib/Bio/WebAgent.pm
 lib/BioPerl.pm
-maintenance/README
-maintenance/authors.pl
-maintenance/check_NAME.pl
-maintenance/check_URLs.pl
-maintenance/cvs2cl_by_file.pl
-maintenance/dependencies.pl
-maintenance/deprecated.pl
-maintenance/find_mod_deps.pl
-maintenance/module_usage.pl
-maintenance/modules.pl
-maintenance/ncbi_blast_switches.pl
-maintenance/perltidy.conf
-maintenance/pod.pl
-maintenance/symlink_script.pl
-maintenance/version.pl
-models/README
-models/biblio.dia
-models/bio_liveseq_variation.dia
-models/bio_map.dia
-models/bio_restriction.dia
-models/bioperl.dia
-models/coordinatemapper.dia
-models/map_proposal.txt
-models/maps_and_markers.dia
-models/popgen.dia
-models/population_proposal.txt
 t/00-compile.t
 t/Align/AlignStats.t
 t/Align/AlignUtil.t
@@ -631,7 +596,6 @@ t/AlignIO/prodom.t
 t/AlignIO/psi.t
 t/AlignIO/selex.t
 t/AlignIO/xmfa.t
-t/Alphabet.t
 t/Annotation/Annotation.t
 t/Annotation/AnnotationAdaptor.t
 t/LocalDB/Fasta.t
@@ -707,7 +671,6 @@ t/Seq/PrimedSeq.t
 t/Seq/Quality.t
 t/Seq/Seq.t
 t/Seq/SimulatedRead.t
-t/Seq/WithQuality.t
 t/SeqFeature/Amplicon.t
 t/SeqFeature/Clone.t
 t/SeqFeature/Collection.t
@@ -769,7 +732,6 @@ t/SeqTools/SeqStats.t
 t/SeqTools/SeqUtils.t
 t/SeqTools/SeqWords.t
 t/Species.t
-t/Symbol.t
 t/Tools/Alignment/Consed.t
 t/Tools/AmpliconSearch.t
 t/Tools/EMBOSS/Palindrome.t

META.json

@@ -136,7 +136,7 @@
          "web" : "https://github.com/bioperl/bioperl-live"
       }
    },
-   "version" : "1.7.4",
+   "version" : "1.7.5",
    "x_Dist_Zilla" : {
       "perl" : {
          "version" : "5.028001"
@@ -346,7 +346,7 @@
                   "branch" : null,
                   "changelog" : "Changes",
                   "signed" : 0,
-                  "tag" : "BioPerl-v1.7.4",
+                  "tag" : "BioPerl-v1.7.5",
                   "tag_format" : "%N-v%v",
                   "tag_message" : "%N-v%v"
                },

META.yml

@@ -99,7 +99,7 @@ resources:
   bugtracker: https://github.com/bioperl/bioperl-live/issues
   homepage: https://metacpan.org/release/BioPerl
   repository: git://github.com/bioperl/bioperl-live.git
-version: 1.7.4
+version: 1.7.5
 x_Dist_Zilla:
   perl:
     version: '5.028001'
@@ -264,7 +264,7 @@ x_Dist_Zilla:
           branch: ~
           changelog: Changes
           signed: 0
-          tag: BioPerl-v1.7.4
+          tag: BioPerl-v1.7.5
           tag_format: '%N-v%v'
           tag_message: '%N-v%v'
         Dist::Zilla::Role::Git::Repo:

Makefile.PL

@@ -145,7 +145,7 @@ my %WriteMakefileArgs = (
     "Test::More" => 0,
     "Test::Weaken" => 0
   },
-  "VERSION" => "1.7.4",
+  "VERSION" => "1.7.5",
   "test" => {
     "TESTS" => "t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t"
   }

debian/changelog

+bioperl (1.7.5-1) unstable; urgency=medium
+
+  * New upstream version
+  * Packaged with routine-update script
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Steffen Moeller <moeller@debian.org>  Sat, 27 Jul 2019 17:55:00 +0200
+
 bioperl (1.7.4-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-12

debian/control

@@ -7,9 +7,9 @@ Uploaders: Charles Plessy <plessy@debian.org>,
 Section: science
 Testsuite: autopkgtest-pkg-perl
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
 # Unnecessary according to lintian, but building with sbuild shows the contrary.
-               libmodule-build-perl (>= 0.420000)
+               libmodule-build-perl
 Build-Depends-Indep: perl,
                      rename,
                      libio-string-perl,
@@ -57,7 +57,7 @@ Build-Depends-Indep: perl,
                      libtest-requiresinternet-perl,
 # Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
                      libxml-sax-expatxs-perl
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/bioperl
 Vcs-Git: https://salsa.debian.org/med-team/bioperl.git
 Homepage: http://www.bioperl.org/
@@ -180,8 +180,6 @@ Recommends: bioperl-run | libbio-perl-run-perl,
 Suggests: bioperl,
           libxml-sax-expatxs-perl
 # Needed to avoid downloading DTDs.
-Breaks: grinder (<< 0.5.3-3~)
-Replaces: grinder (<< 0.5.3-3~)
 Description: BioPerl core perl modules
  BioPerl is a toolkit of perl modules useful in building bioinformatics
  solutions in Perl. It is built in an object-oriented manner so that many

dist.ini

 name = BioPerl
-version = 1.7.4
+version = 1.7.5
 author = See individual modules
 copyright_holder = See individual modules
 license = Perl_5

examples/root/exceptions1.pl

-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # A simple tester script for demonstrating how to throw and catch
 # Error.pm objects. It also shows how to define new types of

examples/root/exceptions2.pl

-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # This shows how Error.pm-based objects can be thrown 
 # by Bio::Root::Root::throw() when Error.pm is available.

examples/root/exceptions3.pl

-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # This shows that Error objects can be subclassed into more specialized types.
 # Bio::Root::FileOpenException is a subclass of  Bio::Root::IOException. 

examples/root/exceptions4.pl

-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # This shows how the examples work when Error.pm isn't installed.
 # It also shows how to supress using Error.pm if it is installed

examples/searchio/custom_writer.pl

-#!/usr/bin/env perl 
+#!/usr/bin/perl
 
 # Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
 # for producing custom output of Blast hit data from a Blast report 

examples/searchio/hspwriter.pl

-#!/usr/bin/env perl 
+#!/usr/bin/perl
 
 # Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
 # for producing tab-delimited output of HSP data from a Blast report 

examples/searchio/rawwriter.pl

-#!/usr/bin/env perl 
+#!/usr/bin/perl
 
 # Demonstrates the use of a SearchIO Blast parser for producing
 # output of raw HSP data from a Blast report input stream.

examples/tools/seq_pattern.pl

-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 #-----------------------------------------------------------------------------
 # PROGRAM : seq_pattern.pl 

lib/Bio/Align/AlignI.pm

@@ -93,10 +93,9 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::AlignI;
-$Bio::Align::AlignI::VERSION = '1.7.4';
+$Bio::Align::AlignI::VERSION = '1.7.5';
 use strict;
 
-
 use base qw(Bio::Root::RootI);
 
 =head1 Modifier methods
@@ -833,38 +832,4 @@ sub set_displayname_normal {
     $self->throw_not_implemented();
 }
 
-=head1 Deprecated methods
-
-=head2 no_residues
-
- Title     : no_residues
- Usage     : $no = $ali->no_residues
- Function  : number of residues in total in the alignment
- Returns   : integer
- Argument  :
- Note      : deprecated in favor of num_residues()
-
-=cut
-
-sub no_residues {
-    # immediate deprecation
-    shift->deprecated();
-}
-
-=head2 no_sequences
-
- Title     : no_sequences
- Usage     : $depth = $ali->no_sequences
- Function  : number of sequence in the sequence alignment
- Returns   : integer
- Argument  : None
- Note      : deprecated in favor of num_sequences()
-
-=cut
-
-sub no_sequences {
-    # immediate deprecation
-    shift->deprecated();
-}
-
 1;

lib/Bio/Align/DNAStatistics.pm

@@ -335,7 +335,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::DNAStatistics;
-$Bio::Align::DNAStatistics::VERSION = '1.7.4';
+$Bio::Align::DNAStatistics::VERSION = '1.7.5';
 use vars qw(%DNAChanges @Nucleotides %NucleotideIndexes
 	    $GapChars $SeqCount $DefaultGapPenalty %DistanceMethods
             $CODONS %synchanges $synsites $Precision $GCChhars);

lib/Bio/Align/PairwiseStatistics.pm

@@ -76,7 +76,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::PairwiseStatistics;
-$Bio::Align::PairwiseStatistics::VERSION = '1.7.4';
+$Bio::Align::PairwiseStatistics::VERSION = '1.7.5';
 use vars qw($GapChars);
 use strict;